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Table 1 Information needed for the tab-delimited input files

From: Prioritising positively selected variants in whole-genome sequencing data using FineMAV

Information needed from the VCF file

Description

Mandatory VCF column

CHROM:POS

Chromosome number:position

Yes

ID

Identifier

Yes

REF

Reference base

Yes

ALT

Alternative base

Yes

AA

Ancestral allele

No

CADD_PHRED

Phred-scaled Combined Annotation Dependent Depletion (CADD) score

No

AF

Allele frequency (AF) for the alternative base. The AF should be reported for each population

No

  1. This information can be extracted from the VCF file and provided in a tab-delimited format for the software to calculate the FineMAV scores